scholarly journals Analysis of the Efficacy and Pharmacological Mechanisms of Action of Zhenren Yangzang Decoction on Ulcerative Colitis Using Meta-Analysis and Network Pharmacology

2021 ◽  
Vol 2021 ◽  
pp. 1-17
Author(s):  
Guosheng Xing ◽  
Yufeng Zhang ◽  
Xinlin Wu ◽  
Hua Wang ◽  
Yan Liu ◽  
...  
Keyword(s):  
Target Genes ◽  
Kegg Pathway ◽  
Meta Analysis ◽  
Mechanisms Of Action ◽  
Functional Enrichment ◽  
Network Pharmacology ◽  
Active Compounds ◽  
Pathway Enrichment ◽  
Active Target ◽  
Protein Protein Interaction

Objective. We analyzed the efficacy and pharmacological mechanisms of action of Zhen Ren Yang Zang decoction (ZRYZD) on ulcerative colitis (UC) using meta-analysis and network pharmacology. Methods. The major databases were searched for randomized controlled trials of ZRYZD for the treatment of UC. Meta-analysis of the efficacy of ZRYZD on UC was conducted using RevMan software. Active compounds and target genes were acquired using the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform. UC-related genes were searched using the GeneCards database. Gene Ontology (GO) functional enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed using RGUI. A compound-target network was constructed using Cytoscape software, and a protein-protein interaction network was constructed using the STRING database. Molecular docking simulations of the macromolecular protein targets and their corresponding ligand compounds were performed using the AutoDock tool and AutoDock Vina software. Results. Meta-analysis revealed that the total effective rate and recovery rate of clinical efficacy were significantly higher in the experimental group than those of the control group. The screening identified 169 active compounds and 277 active target genes for ZRYZD. The 277 active target genes were compared with the 4,798 UC-related genes. This identified 187 active target genes of ZRYZD for UC that correlated with 138 active compounds. GO functional enrichment and KEGG pathway enrichment analyses were performed, and compound-target and protein-protein interaction networks were constructed. The key compounds and key target proteins were then selected. Finally, target protein binding with the corresponding compound was analyzed using molecular docking. Conclusion. Our findings demonstrate the effectiveness and safety of ZRYZD for the treatment of UC and provide insight into the underlying pharmacological mechanisms of action. Furthermore, key compounds were identified, laying the foundation for future studies on ZRYZD for the treatment of UC.

scholarly journals Elucidation of the Mechanisms and Molecular Targets of Lianhuaqingwen for Treatment of COVID-19 Based on Network Pharmacology

2021 ◽  
Vol 9 (4) ◽  
pp. 111-122
Author(s):  
Yan Luo ◽  
Si-ting Gao ◽  
Jun-xiong Cheng ◽  
Wei-jian Xiong ◽  
Wen-Fu Cao
Keyword(s):  
Target Genes ◽  
Molecular Targets ◽  
Core Gene ◽  
Mechanisms Of Action ◽  
Network Pharmacology ◽  
Pathway Network ◽  
Functional Annotations ◽  
Gene Pathway ◽  
Protein Protein Interaction ◽  
Ppi Networks

Lianhuaqingwen (LH) is the widely used in the treatment of Coronavirus disease 2019 (COVID-19). However, its mechanisms of action and molecular targets for treatment of COVID-19 are not clear. The active compounds of LH were collected and their targets were identified through the network pharmacology. The mechanism of compound multi components and multi targets and its relationship with disease are analyzed. COVID-19 targets were obtained by analyzing with TCMSP. In total, 282 active ingredients and 510 targets of LH were identified. Twenty-one target genes associated with LH and COVID-19. Protein-protein interaction (PPI) data were then obtained and PPI networks of LH putative targets and COVID-19-related targets were visualized and merged to identify the candidate targets for LH against COVID-19. Gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis were carried out. The gene-pathway network was constructed to screen the crucial target genes. The functional annotations of target genes were found to be related to immune regulation, host defense, inflammatory reaction and autoimmune diseases and so on. Twenty pathways including immunology, cancer, and cell processing were significantly enriched. Quercetin and luteolin might be the crucial ingredients. IL6 was the core gene and other several genes including IL1B, STAT1, IFNGR1, and NCF1 were the key genes in the gene-pathway network of LH for treatment of COVID-19. The results indicated that LH’s effects against COVID-19 might relate to regulation of immunological function through the specific biological processes and the related pathways. This study demonstrates the application of network pharmacology in evaluating mechanisms of action and molecular targets of complex herbal formulations.

scholarly journals Effect and mechanism of Acoritataninowii Rhizoma and Curcumae Radix on chronic gastritis: a network pharmacology study

2020 ◽  
Author(s):  
Ling Zhang ◽  
Yunkai Dai ◽  
Yuping Li ◽  
Weijing Chen ◽  
Ruliu Li ◽  
...  
Keyword(s):  
Signaling Pathway ◽  
Chronic Gastritis ◽  
Protein Interaction ◽  
Target Genes ◽  
Kegg Pathway ◽  
Network Pharmacology ◽  
Signal Pathways ◽  
Ppi Network ◽  
Pathway Enrichment ◽  
Go Enrichment

Abstract Background Chronic gastritis (CG) is an inflammatory disease which is one of the common diseases of the digestive system. To investigate the mechanisms of herbal pair Acoritataninowii Rhizoma(Shichangpu, AR) and Curcumae Radix༈Yujin, CR༉ in treatment of CG based on the network pharmacology. Methods The possible active ingredients and targets of AR-CR were obtained by the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP). The UniProt database was used to query the human gene corresponding to each target protein. The genes related to CG were collected from the GeneCards database, the OMIM database, the DisGeNET database and the PharmGKB database. Intersected the target genes of AR-CR and CG, then protein-protein interaction(PPI) network was constructed by STRING website. The overlapped genes were subjected to gene ontology༈GO༉enrichment and Kyoto encyclopedia of genes and genomes༈KEGG༉pathway enrichment analyses by David. Results 45 intersection genes were obtained, and there were 40 targets in the PPI network for protein interaction, the kernel targets with Degree ≥ 10 included AKT1, TNF, JUN, MAPK3, MAPK8 and MAPK1. The Go enrichment analysis was mainly related to protein binding, enzyme binding, protein homodimerization activity, etc. The KEGG pathway enrichment analyses mainly involved the Pathways in cancer, TNF signaling pathway, Apoptosis, and VEGF signaling pathway. Conclusion AR-CR might delayed, blocked or reversed the atrophy, intestinal metaplasia, dysplasia and canceration of gastric mucosa by targeting key proteins and signal pathways,achieved the effect of the treatment of CG.

scholarly journals Exploration of Anti-Staphylococcus Aureus Activity and Molecular Mechanism of Wuweixiaoduyin using Network Pharmacology Anti-Staphylococcus Aureus Activity of Wuweixiaoduyin using Network Pharmacology

2021 ◽  
Author(s):  
Kai Huang ◽  
Bigyuan Lin ◽  
Haiyong Ren ◽  
Qifen Mao ◽  
Qiaofeng Guo ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Growth Factor ◽  
Signaling Pathway ◽  
Target Genes ◽  
Therapeutic Targets ◽  
Mitogen Activated Protein Kinase ◽  
Network Pharmacology ◽  
Active Compounds ◽  
Pathway Enrichment ◽  
Aureus Infection

Abstract Background:S. aureus (Staphylococcus aureus) infection imposes a serious burden to global healthcare systems. WWXDY (Wuweixiaoduyin) is a traditional Chinese medicine, and it is usually used to treat infections in China. This study aimed to explore the active compounds, therapeutic targets, key pathways, and potential mechanisms of WWXDY in the treatment of S. aureus infection. Materials & Methods:Data related to active compounds and therapeutic targets of WWXDY for treating S. aureus were collected from DisGeNET, GeneCards, and DrugBank databases. To explore the roles of the active targets in gene function and signaling pathways, KEGG (Kyoto Gene and Genomics Encyclopedia) pathway enrichment and GO (Gene Ontology) analyses of the 122 target genes in the PPI (protein-protein interaction) network were performed. We further performed NP (network pharmacology) by using a network analyzer to screen 30 key targets. Results:A total 92 active compounds of WWXDY were screened. The 122 overlapped genes were found from 785 therapeutic targets and 684 S. aureus-related genes. Besides, 92 active compounds of WWXDY, such as mandenol, ethyllinolenate, eriodyctiol, secologanic dibutylacetal_qt, etc., were identified. The PPI network of the effective ingredients of WWXDY in treating S. aureus infection identified the top 30 genes, including IL-6 (interleukin-6), TNF-α (tumor necrosis factor-α), VEGFA (vascular endothelial growth factor A), AKT1, CXCL8, MAPK3 (mitogen-activated protein kinase 3), TLR (toll-like receptor 4), IL-1β, EGFR (epidermal growth factor receptor), and MMP9 (matrix metalloproteinase-9). Conclusion:The GO functional and KEGG pathway enrichment analyses indicated that 122 overlapped genes were mainly enriched in COVID-19, AGE-RAGE signaling pathway, C-type lectin receptor signaling pathway, Pertussis, and Chagas disease. Our findings indicated the active compounds and therapeutic targets of WWXDY in treating S. aureus infection, as well as its potential mechanisms.

scholarly journals Network Pharmacology Prediction: The Possible Mechanisms of Cinobufotalin against Osteosarcoma

2022 ◽  
Vol 2022 ◽  
pp. 1-9
Author(s):  
Riyu Chen ◽  
Zeyi Guan ◽  
Xianxing Zhong ◽  
Wenzheng Zhang ◽  
Ya Zhang
Keyword(s):  
Survival Curve ◽  
Therapeutic Targets ◽  
Enrichment Analysis ◽  
Functional Enrichment Analysis ◽  
Functional Enrichment ◽  
Network Pharmacology ◽  
Hub Genes ◽  
Survival Prognosis ◽  
Active Compounds ◽  
Protein Protein Interaction

Objective. To explore the active compounds and targets of cinobufotalin (huachansu) compared with the osteosarcoma genes to obtain the potential therapeutic targets and pharmacological mechanisms of action of cinobufotalin on osteosarcoma through network pharmacology. Methods. The composition of cinobufotalin was searched by literature retrieval, and the target was selected from the CTD and TCMSP databases. The osteosarcoma genes, found from the GeneCards, OMIM, and other databases, were compared with the cinobufotalin targets to obtain potential therapeutic targets. The protein-protein interaction (PPI) network of potential therapeutic targets, constructed through the STRING database, was inputted into Cytoscape software to calculate the hub genes, using the NetworkAnalyzer. The hub genes were inputted into the Kaplan-Meier Plotter online database for exploring the survival curve. Functional enrichment analysis was identified using the DAVID database. Results. 28 main active compounds of cinobufotalin were explored, including bufalin, adenosine, oleic acid, and cinobufagin. 128 potential therapeutic targets on osteosarcoma are confirmed among 184 therapeutic targets form cinobufotalin. The hub genes included TP53, ACTB, AKT1, MYC, CASP3, JUN, TNF, VEGFA, HSP90AA1, and STAT3. Among the hub genes, TP53, ACTB, MYC, TNF, VEGFA, and STAT3 affect the patient survival prognosis of sarcoma. Through function enrichment analysis, it is found that the main mechanisms of cinobufotalin on osteosarcoma include promoting sarcoma apoptosis, regulating the cell cycle, and inhibiting proliferation and differentiation. Conclusion. The possible mechanisms of cinobufotalin against osteosarcoma are preliminarily predicted through network pharmacology, and further experiments are needed to prove these predictions.

scholarly journals Network Pharmacology Strategy to Investigate the Pharmacological Mechanism of Siwu Decoction on Primary Dysmenorrhea and Molecular Docking Verification

2021 ◽  
Vol 2021 ◽  
pp. 1-13
Author(s):  
Dandan Jiang ◽  
Xiaoyan Wang ◽  
Lijun Tian ◽  
Yufeng Zhang
Keyword(s):  
Molecular Docking ◽  
Target Genes ◽  
Network Pharmacology ◽  
Primary Dysmenorrhea ◽  
Ppi Network ◽  
Active Compounds ◽  
Docking Simulations ◽  
Active Target ◽  
Target Network ◽  
Compound Target

Objective. To study the pharmacological mechanisms of Siwu decoction (SWD) on primary dysmenorrhea (PDM) and verify with molecular docking. Methods. The  Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP) was utilized to acquire the active compounds and their corresponding target genes. The GeneCards database was utilized in the search for target genes that were associated with PDM. The intersection genes from the active target genes of SWD and those associated with PDM represented the active target genes of SWD that act on PDM. The Gene Ontology (GO) function enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were both carried out by RGUI 3.6.1 and Cytoscape 3.6.0 software. Cytoscape was also utilized for creating a compound-target network, and a protein-protein interaction (PPI) network was created through the STRING database. Molecular docking simulations of the macromolecular protein target receptors and their corresponding compounds were performed using AutoDockTool 1.5.6 and AutoDock Vina software. Results. We identified 14 active compounds as well as 97 active target genes of SWD by using the TCMSP. We compared the 97 active target genes of SWD to the 299 target genes related to PDM, and 23 active target genes for SWD that act on PDM which correlated with 11 active compounds were detected. The compound-target network as well as the PPI network were created, in addition to selecting the most essential compounds and their targets in order to create a key compound-target network. The most essential compounds were kaempferol, beta-sitosterol, stigmasterol, and myricanone. The key targets were AKT1, PTGS2, ESR1, AHR, CASP3, and PGR. Lastly, molecular docking was used to confirm binding of the target with its corresponding compound. Conclusion. The pharmacological mechanisms of SWD that act on PDM were investigated, and the active compounds in the SWD for treating PDM were further verified.

scholarly journals Network Pharmacology Analysis of the active components and anticancer targets of Rhubarb

2021 ◽  
Author(s):  
Hu Junrui ◽  
Duan Yongqiang ◽  
Cui Gongning ◽  
Luo Qiang ◽  
Xi Shanshan ◽  
...  
Keyword(s):  
Pathway Analysis ◽  
Drug Targets ◽  
Target Genes ◽  
Kegg Pathway ◽  
Enrichment Analysis ◽  
Network Pharmacology ◽  
Active Components ◽  
Active Compounds ◽  
Cellular Targets ◽  
Kegg Pathway Analysis

AbstractTo investigate the mechanisms and active components governing the anticancer activity of rhubarb.The TCMSP database was screened to identify the active components of rhubarb and Swiss target predictions were generated to predict their cellular targets. TTD and OMIM databases were used to predict tumor-related target genes. "Cytoscape" was used to construct drug targets. PPI network analysis, GO enrichment analysis and KEGG pathway analysis of the key targets were investigated using String and David databases. A total of 33 components and 116 corresponding targets were screened. Amongst them, the key active compounds in rhubarb included emodin, aloe emodin, β-sitosterol, emodin methyl ether and rhein, which were predicted to target TP53, AKT1, STAT3, PIK3CA, HRAS, and VEGFA. GO analysis revealed that the cellular targets clustered into 159 biological processes, including those involved in cellular composition (n=24) and molecular functions (n=42, P<0.01). KEGG pathway analysis revealed 85 (P < 0.01) pathways related to cancer. The active compounds in rhubarb target TP53, AKT1 and PIK3CA. Rhubarb therefore regulates cancer development through an array of biological pathways.

scholarly journals Uncovering the pharmacological mechanism of strychnos nux-uomical in the treatment of peripheral neuropathy based on a network pharmacology approach

2021 ◽  
Author(s):  
JingJing Xiang ◽  
Chen-Jun Lin ◽  
Yu Zhang ◽  
Ni Zhu ◽  
Jian-Ping Shen ◽  
...  
Keyword(s):  
Peripheral Neuropathy ◽  
Target Genes ◽  
Kegg Pathway ◽  
Chinese Herb ◽  
Target Prediction ◽  
Network Pharmacology ◽  
Pharmacokinetic Parameters ◽  
Pathway Enrichment Analysis ◽  
Pathway Enrichment ◽  
Underlying Mechanisms

Abstract Background: Strychnos nux-uomical (Ma Qianzi in pinyin), a classic chinese herb, has been extensively used to treat peripheral neuropathy in clinical practice in china for many years. However, the pharmacological mechanisms of strychnos nux-uomical remain vague. The aim of this study was to decrypt the underlying mechanisms of strychnos nux-uomical in the treatment of peripheral neuropathy using a systems harmacology approach.Methods: Using pharmacokinetic parameters [oral bioavailability (OB)≥30% and drug likeness (DL)≥0.18] of traditional chinese medicine system pharmacology platform (TCMSP) to screen the active ingredient of strychnos nux-uomical, and then integrating target prediction human gene database to predict and screen its target genes for the treatment of strychnos nux-uomical, network topology attribute analysis software cytoscape 3.6.0 was utilized to construct the active components-peripheral neuropath targets network. String database and cytoscape software were used to draw the protein interaction network. Finally gene ontology (GO) and kyoto encyclopedia of genes and genomes (KEGG) pathway enrichment analyses by panther database. Results: A total of 13 potential active ingredients were screened based on their OB and DL parameters, and 72 core targets were related to disease target. The results of pathway enrichment analysis indicated that putative targets of strychnos nux-uomical mostly participated in various pathways associated with cellular process, response to stimulus, biological regulation, metabolic process, localization. The putative targets of strychnos nux-uomical (endothelial growth factor, tumor necrosis factor-α, interleukin-10, interleukin-6, interleukin 1β and so on) were recognized as active factors involved in the main biological functions of treatment, which implied that these were involved in the underlying mechanisms of strychnos nux-uomical on peripheral neuropathy.Conclusions: In this study, a network pharmacology-based strategy integrating target prediction, network construction, GO and KEGG pathway enrichment analyses, was adopted to predict the targets of strychnos nux-uomical relevant to the treatment of peripheral neuropathy and to further explore the involved pharmacological mechanisms.

scholarly journals Network Pharmacology Reveals the Molecular Mechanism of Cuyuxunxi Prescription in Promoting Wound Healing in Patients with Anal Fistula

2019 ◽  
Vol 2019 ◽  
pp. 1-9 ◽  
Author(s):  
Yin Qu ◽  
Zhijun Zhang ◽  
Yafeng Lu ◽  
De Zheng ◽  
Yang Wei
Keyword(s):  
Chinese Medicine ◽  
Traditional Chinese Medicine ◽  
Target Genes ◽  
Herbal Medicines ◽  
Enrichment Analysis ◽  
Functional Enrichment Analysis ◽  
Functional Enrichment ◽  
Network Pharmacology ◽  
Surgical Wound ◽  
Active Compounds

Background. The healing process of the surgical wound of anal fistulotomy is much slower because of the presence of stool within the wound. Cuyuxunxi (CYXX) prescription is a Chinese herbal fumigant that is being used to wash surgical wound after anal fistulotomy. This study aimed at investigating the molecular mechanism of CYXX prescription using a network pharmacology-based strategy. Materials and Methods. The active compounds in each herbal medicine were retrieved from the traditional Chinese medicine systems pharmacology (TCMSP) database and in Traditional Chinese Medicine Integrated Database (TCMID) analysis platform based on the criteria of oral bioavailability ≥40% and drug-likeness ≥0.2. The disease-related target genes were extracted from the Comparative Toxicogenomics Database. Protein-protein interaction network was built for the overlapped genes as well as functional enrichment analysis. Finally, an ingredient-target genes-pathway network was built by integrating all information. Results. A total of 375 chemical ingredients of the 5 main herbal medicines in CYXX prescription were retrieved from TCMSP database and TCMID. Among the 375 chemical ingredients, 59 were active compounds. Besides, 325 target genes for 16 active compounds in 3 herbal medicines were obtained. Functional enrichment analysis revealed that these overlapped genes were significantly related with immune response, biosynthesis of antibiotics, and complement and coagulation cascades. A comprehensive network which contains 133 nodes (8 disease nodes, 3 drug nodes, 8 ingredients, 103 target gene nodes, 7 GO nodes, and 4 pathway nodes) was built. Conclusion. The network built in this study might aid in understanding the action mechanism of CYXX prescription at molecular level to pathway level.

scholarly journals Exploring the Potential Mechanism of Chuanxiong Rhizoma Treatment for Migraine Based on Systems Pharmacology

2021 ◽  
Vol 2021 ◽  
pp. 1-15
Author(s):  
Xianhua Wen ◽  
Yuncheng Gu ◽  
Beili Chen ◽  
Feipeng Gong ◽  
Wenting Wu ◽  
...  
Keyword(s):  
Drug Targets ◽  
Treatment Process ◽  
Kegg Pathway ◽  
Systems Pharmacology ◽  
Active Compounds ◽  
Pathway Enrichment ◽  
Protein Protein Interaction ◽  
Target Disease ◽  
Tcm Theory ◽  
Drug Compound

Migraine is a disease whose aetiology and mechanism are not yet clear. Chuanxiong Rhizoma (CR) is employed in traditional Chinese medicine (TCM) to treat various disorders. CR is effective for migraine, but its active compounds, drug targets, and exact molecular mechanism remain unclear. In this study, we used the method of systems pharmacology to address the above issues. We first established the drug-compound-target-disease (D-C-T-D) network and protein-protein interaction (PPI) network related to the treatment of migraine with CR and then established gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses. The results suggest that the treatment process may be related to the regulation of inflammation and neural activity. The docking results also revealed that PTGS2 and TRPV1 could directly bind to the active compounds that could regulate them. In addition, we found that CR affected 11 targets that were more highly expressed in the liver or heart but were the lowest in the whole brain. It also expounds the description of CR channel tropism in TCM theory from these angles. These findings not only indicate that CR can be developed as a potential effective drug for the treatment of migraine but also demonstrate the application of systems pharmacology in the discovery of herbal-based disease therapies.

scholarly journals Identification of crucial genes in metastatic osteosarcoma and prognostic biomarker in osteosarcoma patients

2020 ◽  
Author(s):  
Weihao Wang ◽  
Zhaoyong Liu ◽  
Weiqing Lu ◽  
Huancheng Guo ◽  
Chunbin Zhou ◽  
...  
Keyword(s):  
Gene Expression ◽  
Target Genes ◽  
Kegg Pathway ◽  
Prognostic Biomarker ◽  
Clinical Information ◽  
Diagnostic Value ◽  
Functional Enrichment ◽  
Pathway Enrichment ◽  
Metastatic Osteosarcoma ◽  
Target Database

Abstract Background Osteosarcoma is still a challenging cancer that poses a huge threat to human health worldwide, especially in young people. The aim of this study was to identify prognostic genes associated with neoplasm metastasis in osteosarcoma, and construct a prognostic nomogram to help the orthopedist to assess prognosis of osteosarcoma patients.Methods Gene expression and clinical information were extracted from the TARGET database. Differentially expressed genes (DEGs) associated with osteosarcoma metastasis were identified and subjected to GO functional and KEGG pathway enrichment analyses. Survival and Cox analyses were used to identify prognostic genes.Results First, 214 DEGs were identified as crucial genes associated with osteosarcoma metastasis. Then functional enrichment analyses showed that DEGs were enriched in cell-cell signaling, inflammatory response, and immune response. Survival and Cox analyses identified five prognostic genes (MUC17, MYC, TAC4, HERC5, OR8G5) that were related to the prognosis of patients. This five-genes signature has a great diagnostic value for prognosis because it was not affected by age at diagnosis, gender, metastasis or relapse.Conclusions The present study identifies five target genes related to the metastasis of osteosarcoma. This five-genes signature can be used to predict the prognosis of osteosarcoma patients and may become new potential therapeutic targets for the treatment of osteosarcoma.

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